After a chance-laden but goalless first half, German international Marko Marin gave the visitors the lead soon after the restart, but a brace on his 19th birthday from January signing Anton Forrester meant a first win in 2013 for the development squad.
Speaking to Rovers Player
after the game, boss Bowyer was impressed with how his side went about their work on a chilly night.
"It was a great performance against a very talented team," said Bowyer.
"We had a game plan and we stuck to the game plan quite well.
"In the first half it was always good to be going in with a clean sheet and then I thought we responded magnificent to them scoring.
"You always worry when Chelsea score the first goal but I thought we did very well and it was two great strikes from Anton. The second one was a little fortunate with the way it came about but he finished it off very well.
"He worked hard on his own up there but we are delighted with him. He's got something a little bit different for us that we haven't had for a while.
"In a lot of the Rovers Reserve teams we've been missing a young centre forward and he's come in and started off quite nicely. We just got to keep on top of him and push him on. We're delighted with how he has started."
Highlights of the win will be available on Rovers Player
later today. The Reserves are back in action next Monday night at Leigh when Sunderland are the visitors.